Research workbench

Human SARM1 inhibitory state bounded with inhibitor dhnn

Analyse Human SARM1 inhibitory state bounded with inhibitor dhnn in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7DJT
Type: protein
Length: 5,112 residues
Chains: 8
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NAD(+) hydrolase SARM1
EC: 3.2.2.6, 3.2.2.-
UniProt: Q6SZW1
Ligands: H8L, O
Pockets: 20 · best druggability 0.84

Structure

electron microscopy · 1 distinct chain · 55% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	NAD(+) hydrolase SARM1 (EC 3.2.2.6, 3.2.2.-)	protein	639	55% helix, 3% strand	Q6SZW1

Ligands and binding sites

H8L · O3-methyl O5-(2-methylpropyl) 2,6-dimethyl-4-[2-(oxidanylamino)phenyl]pyridine-3,5-dicarboxylate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
O · Oxygen atom · ion · 16 copies · chains A, B, C, D, E, F, G, H

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1021	0.84	0.85	104	empty
2	973	0.84	0.85	108	empty
3	901	0.83	0.85	86	empty
4	865	0.83	0.85	92	empty
5	627	0.81	0.86	64	empty

Interfaces

16 interfaces between chains.

E–F · 2351 Å² buried · 13 hydrogen bonds · protein-protein
F–G · 2347 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 2346 Å² buried · 12 hydrogen bonds · protein-protein
D–E · 2345 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 2344 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 covalent (covalent ligand).

Compared structures

7DJT · Human SARM1 inhibitory state bounded with inhibitor dHNN · the same entry in another collection · chain F against F, TM-score 1.00
Q6SZW1 · AlphaFold monomer V2.0 prediction for NAD(+) hydrolase SARM1 (Q6SZW1) · a predicted model of the same protein · chain C against A, TM-score 0.95

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q6SZW1
Elsewhere: RCSB PDB 7DJT · PDBe 7DJT · UniProt Q6SZW1

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.